You're trying to inverse transform your raw data rather than your
transformed data, which is x, not samp.


On Thu, Jul 10, 2014 at 11:14 AM, Allenby, Mark <mark.allenby@imperial.ac.uk
> wrote:

> All,
>
> I have been trying to transform my data by  logicle and inverse logicle
> transformations. However, even when I copy the logicle transformation
> parameters the software estimates, the transform function still does not
> work, and brings up the warning NAs introduced by coercion. I am wondering
> if I am defining my inputs in improper form? Could anyone help me out? An
> example is below:
>
> ------------------
>
> samp <- read.FCS(file.name, transformation=FALSE)
> lgcl <- estimateLogicle(samp, logchannels)
> x <- transform(x,lgcl)
>
> Wset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$w
> Tset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$t
> Mset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$m
> Aset <- as.list(environment(lgcl@transforms "488-530/30-A"@f))$a
>
> logicle  <- logicleTransform(t = Tset, w = Wset, m = Mset, a = Aset,
> 'logicle')
> invLgcl <- inverseLogicleTransform(trans = logicle)
> samp <- transform(samp, "488-530/30-A" = invLgcl("488-530/30-A"))
>
> ----------------------
>
> The final line produces the warning:
>
> 1: In invLgcl("488-530/30-A") : NAs introduced by coercion
>
> Would anyone have an idea about what I might be doing incorrectly? I am
> new to R and flowCore, so it could be a basic problem I am overlooking.
> Thank you all so much for your help.
>
> Sincerely,
>
> Mark
> PhD at ICL
>
> -----Original Message-----
> From: Allenby, Mark
> Sent: 10 July 2014 16:11
> To: bioconductor@r-project.org
> Subject: FlowCore: Extracting parameters from estimateLogicle
>
> All,
>
> Is there a way to extract the A, T, M, W logicle parameters from the
> estimateLogicle function?
>
> i.e. lgcl <- estimateLogicle(samp, logchannels) and extract parameters
> estimated from lgcl.
>
> Mark
>
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-- 
Greg Finak, PhD
Staff Scientist
Vaccine and Infectious Disease Division
Fred Hutchinson Cancer Research Center
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